Invalid SM tag in sam record

[kevyin]

SNAP seems to put some @rg-* tags into the alignment section
This shouldn't happen for SM and PL tags as they are either not defined or have different meanings.

According to the SAMFile Spec
@RG-SM is the Sample name
SNAP will put this into the alignment section as
SM:Z:SomeSampleName
However SM is defined in the SAMFile spec as "SM i Template-independent mapping quality"
which has type "i" (Singed 32-bit integer).
Tools such as qProfiler trying to convert the string into integer will fail.

Another tag is @RG-PL
Which appears as
PL:Z:SomePlatform
But this is actually not a defined TAG in the spec

An Example record that fails in qProfiler

HWI-D00119:67:H7NV5ADXX:1:2107:1489:93313   77  *   0   0   *   *   0   0   ATAGAAGAGTGCCGCTCCGAGTTGGAGGTGCTGCAGCAGAGGCGGAATCCGGGGGAACGGGAATGGGGAAACCTGCCCTCCTTGTTCGAAGCCGTCAGCAA   ?@@DDDBA:2<DFHA<GI<GH???C9DBH?<9?<D;?98B#############################################################   LB:Z:library    PG:Z:SNAP   RG:Z:1  NM:i:0  SM:Z:jda    PU:Z:AFAKEFC1D_2_jda_Human_NULL_TEST_jd_chr21